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I-TASSER results for job id Rv2616

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)
 Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.13 10 3nmnA PYV Rep, Mult 56,78,84,87,89,102,104,114,150,154,155
20.06 4 4a81A 2AN Rep, Mult 33,35,47,102,118,131,133,151,155,156,159,160
30.05 4 2flhC ZEA Rep, Mult 48,51,79,86,88,102,118,155
40.04 3 2c21B NI Rep, Mult 110,132
50.03 2 2p7pD SO4 Rep, Mult 28,30
60.03 2 4q0kA GA3 Rep, Mult 48,54,57,78,80,87,118,154,155,158
70.03 2 4ryvA ZEA Rep, Mult 30,32,134,136,148,149,152
80.01 1 1bv10 III Rep, Mult 46,48,51,52,62,63,64,65,68,69,70,93,95
90.01 1 3njoC PYV Rep, Mult 78,80,84,87,89,150,154
100.01 1 1pmmA PLP Rep, Mult 136,137
110.01 1 1w1yA TYP Rep, Mult 104,106
120.01 1 2qimA ZEA Rep, Mult 30,32,34,102,116,132,134,151
130.01 1 3lunB CA Rep, Mult 108,109,114
140.01 1 4qipA SDS Rep, Mult 34,77,79,88,100,118,152,155,156
150.01 1 3ssnA MVI Rep, Mult 148,155
160.01 1 1fipA III Rep, Mult 149,150
170.01 1 3c0vC TBR Rep, Mult 93,95,99,117

Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.1232vq5A0.6322.920.0870.8074.2.1.78NA
20.0601aamA0.4824.640.0070.7352.6.1.1NA
30.0602pmgB0.3664.690.0580.6025.4.2.2NA
40.0601ndoA0.5464.150.0840.8191.14.12.12NA
50.0601im0A0.4954.250.0400.7113.1.1.32,3.1.1.4NA
60.0601z01A0.5903.620.0380.8251.14.13.6153
70.0601bibA0.5204.440.0830.7716.3.4.15NA
80.0602ewnA0.5274.220.0900.7716.3.4.15NA
90.0603mebA0.5034.650.0270.8192.6.1.1NA
100.0602ej9A0.4794.100.0400.6936.3.4.15NA
110.0601dpbA0.4914.230.0530.7292.3.1.12NA
120.0601sczA0.4884.200.0530.7232.3.1.61NA
130.0601kfqB0.4793.810.0300.6815.4.2.2NA
140.0601b5sA0.4904.220.0600.7292.3.1.12NA
150.0601xl7B0.5054.440.0410.7832.3.1.137NA
160.0601aatA0.3335.360.0260.5842.6.1.1NA
170.0603l60A0.5004.130.0870.7292.3.1.12NA
180.0602cghB0.5034.410.0760.7596.3.4.15NA
190.0601b5sE0.4904.220.0600.7292.3.1.12115
200.0601xl7A0.3385.740.0140.6212.3.1.137135

(a)CscoreEC is the confidence score for the EC number prediction. CscoreEC values range in between [0-1];
where a higher score indicates a more reliable EC number prediction.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided
by length of the query protein.

  Gene Ontology (GO) terms

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.220.7313.070.090.933nefA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
10.220.6592.450.100.783q63F GO:0006950
20.210.6372.590.090.781xn5A GO:0006950
30.210.7323.360.070.964oicA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
40.200.6662.950.090.863pu2B GO:0006950
50.200.6223.170.090.802leqA GO:0006950
60.190.6472.940.070.824c94A GO:0006952 GO:0009607
70.190.7213.330.100.943kdhA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
80.180.6642.380.080.801z94B GO:0006950
90.170.6262.690.080.772m89A GO:0006950
100.170.6462.900.080.804fpwA GO:0006950
110.160.6522.930.070.832flhB GO:0006952 GO:0009607
120.160.6452.880.060.812wqlA GO:0006952 GO:0009607
130.160.6573.210.100.834jdlB GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0043086 GO:0080163
140.160.7242.580.070.893w9rA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
150.150.6512.710.070.813putB GO:0006950
160.150.7103.280.100.923k3kA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042802 GO:0042803 GO:0043086 GO:0080163
170.150.6362.690.100.781xn6A GO:0006950
180.150.6823.060.090.871xuvA GO:0006950
190.150.6552.500.100.803cnwA GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
200.150.6453.080.090.822nn5A GO:0006950
210.150.6602.550.100.804n0gC GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
220.140.6562.720.090.813q64A GO:0006950
230.140.6472.980.050.832qimA GO:0006952 GO:0009607 GO:0046872
240.140.6482.750.090.813otlA GO:0006950
250.140.6662.560.060.835c9yA GO:0006952 GO:0009607
260.130.6772.610.050.833rt0C GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
270.120.6372.880.080.834m9bA GO:0006952 GO:0009607
280.110.5713.360.100.752kewA GO:0006950
290.110.6442.990.070.802luzA GO:0006950
300.090.6943.580.070.933ojiB GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
310.090.6512.860.080.845i8fA GO:0006952 GO:0009607
320.080.6452.840.070.822vneA GO:0006952 GO:0009607 GO:0009820 GO:0016829 GO:0050474
330.080.6102.440.120.732lcgA GO:0006950
340.080.6572.650.070.831ifvA GO:0006952 GO:0009607 GO:0016787
350.070.6412.780.050.801xfsA GO:0006950


Consensus prediction of GO terms
 
Molecular Function GO:0042802 GO:0046983 GO:0004864 GO:0004872 GO:0010427
GO-Score 0.45 0.45 0.39 0.39 0.39
Biological Processes GO:0006950 GO:0080163 GO:0043086 GO:0009738
GO-Score 0.51 0.39 0.39 0.39
Cellular Component GO:0071944 GO:0005737 GO:0005634
GO-Score 0.45 0.39 0.39

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.